The Jalview Desktop relies on a number of third-party libraries.
These can be found in the lib directory, with additional compile
time dependencies in the utils directory.

A number of sources have also been adapted for incorporation into Jalview's source tree

ext.edu.ucsf.rbvi.strucviz2 includes sources originally developed by Scooter Morris and Nadezhda Doncheva for the Cytoscape StructureViz2 plugin. It is released under the Berkley license and we hereby acknowledge its original copyright is held by the UCSF Computer Graphics Laboratory
 and the software was developed with support by the NIH National Center for Research Resources, grant P41-RR01081. 

Licencing information for each library is given below:

JGoogleAnalytics_0.3.jar	APL 2.0 License - http://code.google.com/p/jgoogleanalytics/
Jmol-12.1.13.jar	GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/
activation.jar	
apache-mime4j-0.6.jar
axis.jar
castor-1.1-cycle-xml.jar
commons-codec-1.3.jar
commons-discovery.jar
commons-logging-1.1.1.jar
commons-logging.jar
httpclient-4.0.3.jar
httpcore-4.0.1.jar
httpmime-4.0.3.jar
jaxrpc.jar
jdas-1.0.4.jar : Apache License - built from http://code.google.com/p/jdas/ (29th Feb 2012)
jhall.jar
jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12
log4j-1.2.8.jar
mail.jar
miglayout-4.0-swing.jar	BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt
min-jaba-client.jar
regex.jar
saaj.jar
spring-core-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
spring-web-3.0.5.RELEASE.jar : Apache License: jdas runtime dependencies retrieved via maven
vamsas-client.jar
wsdl4j.jar
xercesImpl.jar
xml-apis.jar
json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised)

Additional dependencies

examples/javascript/deployJava.js : http://java.com/js/deployJava.js
examples/javascript/jquery*.js : BSD license
examples/javascript/jshashtable-2.1.js : Apache License

Tools not bundled with Jalview source
jbake (http://jbake.org MIT license) was used to build the JalviewLite examples pages found in the examples directory.